With original MMRd types| ? (N=5) |
Complex (N=11) |
MLH1_PMS2 (N=251) |
MSH2_MSH6 (N=70) |
MSH6 (N=12) |
NORMAL (N=19) |
PMS2 (N=13) |
Total (N=381) |
|
|---|---|---|---|---|---|---|---|---|
| Age (years) | ||||||||
| Mean (SD) | 64.4 (12.8) | 63.8 (19.9) | 67.9 (13.2) | 56.8 (14.1) | 64.5 (11.2) | 61.1 (14.5) | 54.3 (16.7) | 64.8 (14.4) |
| Median [Min, Max] | 63.0 [46.0, 77.0] | 70.0 [26.0, 88.0] | 71.0 [25.0, 90.0] | 55.0 [30.0, 90.0] | 67.0 [36.0, 76.0] | 65.0 [31.0, 87.0] | 48.0 [37.0, 84.0] | 67.0 [25.0, 90.0] |
| Race | ||||||||
| BLACK OR AFRICAN AMERICAN | 1 (20.0%) | 0 (0%) | 15 (6.0%) | 4 (5.7%) | 0 (0%) | 1 (5.3%) | 1 (7.7%) | 22 (5.8%) |
| PT REFUSED TO ANSWER | 1 (20.0%) | 0 (0%) | 6 (2.4%) | 1 (1.4%) | 0 (0%) | 1 (5.3%) | 0 (0%) | 9 (2.4%) |
| WHITE | 3 (60.0%) | 8 (72.7%) | 208 (82.9%) | 57 (81.4%) | 10 (83.3%) | 16 (84.2%) | 9 (69.2%) | 311 (81.6%) |
| ASIAN-FAR EAST/INDIAN SUBCONT | 0 (0%) | 2 (18.2%) | 11 (4.4%) | 4 (5.7%) | 1 (8.3%) | 1 (5.3%) | 3 (23.1%) | 22 (5.8%) |
| OTHER | 0 (0%) | 1 (9.1%) | 9 (3.6%) | 4 (5.7%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 15 (3.9%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 0 (0%) | 2 (0.8%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (0.5%) |
| Ethnicity | ||||||||
| Non-Spanish; Non-Hispanic | 5 (100%) | 8 (72.7%) | 215 (85.7%) | 58 (82.9%) | 11 (91.7%) | 18 (94.7%) | 11 (84.6%) | 326 (85.6%) |
| "Spanish NOS; Hispanic NOS, Latino NOS" | 0 (0%) | 2 (18.2%) | 14 (5.6%) | 8 (11.4%) | 1 (8.3%) | 1 (5.3%) | 1 (7.7%) | 27 (7.1%) |
| Dominican Republic | 0 (0%) | 1 (9.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.3%) |
| 0 | 0 (0%) | 0 (0%) | 3 (1.2%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) | 5 (1.3%) |
| Puerto Rican | 0 (0%) | 0 (0%) | 2 (0.8%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (0.5%) |
| Unknown whether Spanish or not | 0 (0%) | 0 (0%) | 17 (6.8%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 20 (5.2%) |
| Tumor Purity (%) | ||||||||
| Mean (SD) | 48.0 (19.2) | 38.2 (12.7) | 38.3 (16.0) | 39.6 (15.8) | 39.6 (16.3) | 47.2 (17.0) | 38.8 (19.4) | 39.2 (16.1) |
| Median [Min, Max] | 50.0 [20.0, 70.0] | 30.0 [25.0, 60.0] | 40.0 [10.0, 90.0] | 40.0 [5.00, 80.0] | 30.0 [25.0, 80.0] | 50.0 [20.0, 70.0] | 35.0 [10.0, 70.0] | 40.0 [5.00, 90.0] |
| Missing | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) | 3 (0.8%) |
| Cancer Type | ||||||||
| Bladder | 1 (20.0%) | 0 (0%) | 0 (0%) | 5 (7.1%) | 2 (16.7%) | 0 (0%) | 1 (7.7%) | 9 (2.4%) |
| Endometrial | 1 (20.0%) | 1 (9.1%) | 62 (24.7%) | 14 (20.0%) | 1 (8.3%) | 4 (21.1%) | 0 (0%) | 83 (21.8%) |
| Esophagogastric | 2 (40.0%) | 1 (9.1%) | 33 (13.1%) | 4 (5.7%) | 0 (0%) | 2 (10.5%) | 0 (0%) | 42 (11.0%) |
| Small Bowel | 1 (20.0%) | 0 (0%) | 4 (1.6%) | 2 (2.9%) | 0 (0%) | 1 (5.3%) | 4 (30.8%) | 12 (3.1%) |
| Colon | 0 (0%) | 9 (81.8%) | 118 (47.0%) | 19 (27.1%) | 4 (33.3%) | 7 (36.8%) | 4 (30.8%) | 161 (42.3%) |
| Biliary | 0 (0%) | 0 (0%) | 5 (2.0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 6 (1.6%) |
| Colorectal | 0 (0%) | 0 (0%) | 10 (4.0%) | 5 (7.1%) | 3 (25.0%) | 4 (21.1%) | 1 (7.7%) | 23 (6.0%) |
| CUP | 0 (0%) | 0 (0%) | 5 (2.0%) | 0 (0%) | 0 (0%) | 1 (5.3%) | 0 (0%) | 6 (1.6%) |
| Other | 0 (0%) | 0 (0%) | 2 (0.8%) | 5 (7.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 7 (1.8%) |
| Ovarian | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 4 (1.0%) |
| Pancreas | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 4 (1.0%) |
| Prostate | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 4 (1.0%) |
| Rectal | 0 (0%) | 0 (0%) | 9 (3.6%) | 10 (14.3%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 20 (5.2%) |
| Sample Type | ||||||||
| Metastasis | 1 (20.0%) | 1 (9.1%) | 29 (11.6%) | 6 (8.6%) | 2 (16.7%) | 4 (21.1%) | 2 (15.4%) | 45 (11.8%) |
| Mixed | 1 (20.0%) | 1 (9.1%) | 17 (6.8%) | 5 (7.1%) | 2 (16.7%) | 1 (5.3%) | 1 (7.7%) | 28 (7.3%) |
| Primary | 3 (60.0%) | 9 (81.8%) | 205 (81.7%) | 59 (84.3%) | 8 (66.7%) | 14 (73.7%) | 10 (76.9%) | 308 (80.8%) |
With MMRd types collapsed by Multiplex or not| Singleton (N=25) |
? (N=5) |
Multiplex (N=332) |
NORMAL (N=19) |
Total (N=381) |
|
|---|---|---|---|---|---|
| Age (years) | |||||
| Mean (SD) | 59.2 (15.0) | 64.4 (12.8) | 65.4 (14.3) | 61.1 (14.5) | 64.8 (14.4) |
| Median [Min, Max] | 64.0 [36.0, 84.0] | 63.0 [46.0, 77.0] | 68.0 [25.0, 90.0] | 65.0 [31.0, 87.0] | 67.0 [25.0, 90.0] |
| Race | |||||
| ASIAN-FAR EAST/INDIAN SUBCONT | 4 (16.0%) | 0 (0%) | 17 (5.1%) | 1 (5.3%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 1 (4.0%) | 1 (20.0%) | 19 (5.7%) | 1 (5.3%) | 22 (5.8%) |
| OTHER | 1 (4.0%) | 0 (0%) | 14 (4.2%) | 0 (0%) | 15 (3.9%) |
| WHITE | 19 (76.0%) | 3 (60.0%) | 273 (82.2%) | 16 (84.2%) | 311 (81.6%) |
| PT REFUSED TO ANSWER | 0 (0%) | 1 (20.0%) | 7 (2.1%) | 1 (5.3%) | 9 (2.4%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 0 (0%) | 2 (0.6%) | 0 (0%) | 2 (0.5%) |
| Ethnicity | |||||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 2 (8.0%) | 0 (0%) | 24 (7.2%) | 1 (5.3%) | 27 (7.1%) |
| Non-Spanish; Non-Hispanic | 22 (88.0%) | 5 (100%) | 281 (84.6%) | 18 (94.7%) | 326 (85.6%) |
| Unknown whether Spanish or not | 1 (4.0%) | 0 (0%) | 19 (5.7%) | 0 (0%) | 20 (5.2%) |
| 0 | 0 (0%) | 0 (0%) | 5 (1.5%) | 0 (0%) | 5 (1.3%) |
| Dominican Republic | 0 (0%) | 0 (0%) | 1 (0.3%) | 0 (0%) | 1 (0.3%) |
| Puerto Rican | 0 (0%) | 0 (0%) | 2 (0.6%) | 0 (0%) | 2 (0.5%) |
| Tumor Purity (%) | |||||
| Mean (SD) | 39.2 (17.6) | 48.0 (19.2) | 38.6 (15.8) | 47.2 (17.0) | 39.2 (16.1) |
| Median [Min, Max] | 30.0 [10.0, 80.0] | 50.0 [20.0, 70.0] | 40.0 [5.00, 90.0] | 50.0 [20.0, 70.0] | 40.0 [5.00, 90.0] |
| Missing | 0 (0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 3 (0.8%) |
| Cancer Type | |||||
| Colon | 8 (32.0%) | 0 (0%) | 146 (44.0%) | 7 (36.8%) | 161 (42.3%) |
| Biliary | 1 (4.0%) | 0 (0%) | 5 (1.5%) | 0 (0%) | 6 (1.6%) |
| Bladder | 3 (12.0%) | 1 (20.0%) | 5 (1.5%) | 0 (0%) | 9 (2.4%) |
| Colorectal | 4 (16.0%) | 0 (0%) | 15 (4.5%) | 4 (21.1%) | 23 (6.0%) |
| CUP | 0 (0%) | 0 (0%) | 5 (1.5%) | 1 (5.3%) | 6 (1.6%) |
| Endometrial | 1 (4.0%) | 1 (20.0%) | 77 (23.2%) | 4 (21.1%) | 83 (21.8%) |
| Esophagogastric | 0 (0%) | 2 (40.0%) | 38 (11.4%) | 2 (10.5%) | 42 (11.0%) |
| Other | 0 (0%) | 0 (0%) | 7 (2.1%) | 0 (0%) | 7 (1.8%) |
| Ovarian | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Pancreas | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Prostate | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Rectal | 1 (4.0%) | 0 (0%) | 19 (5.7%) | 0 (0%) | 20 (5.2%) |
| Small Bowel | 4 (16.0%) | 1 (20.0%) | 6 (1.8%) | 1 (5.3%) | 12 (3.1%) |
| Sample Type | |||||
| Metastasis | 4 (16.0%) | 1 (20.0%) | 36 (10.8%) | 4 (21.1%) | 45 (11.8%) |
| Mixed | 3 (12.0%) | 1 (20.0%) | 23 (6.9%) | 1 (5.3%) | 28 (7.3%) |
| Primary | 18 (72.0%) | 3 (60.0%) | 273 (82.2%) | 14 (73.7%) | 308 (80.8%) |
With MMRd types collapsed by MSH6 or not| MSH6 (N=82) |
Not_MSH6 (N=299) |
Total (N=381) |
|
|---|---|---|---|
| Age (years) | |||
| Mean (SD) | 57.9 (13.9) | 66.6 (14.0) | 64.8 (14.4) |
| Median [Min, Max] | 56.5 [30.0, 90.0] | 70.0 [25.0, 90.0] | 67.0 [25.0, 90.0] |
| Race | |||
| ASIAN-FAR EAST/INDIAN SUBCONT | 5 (6.1%) | 17 (5.7%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 4 (4.9%) | 18 (6.0%) | 22 (5.8%) |
| OTHER | 5 (6.1%) | 10 (3.3%) | 15 (3.9%) |
| PT REFUSED TO ANSWER | 1 (1.2%) | 8 (2.7%) | 9 (2.4%) |
| WHITE | 67 (81.7%) | 244 (81.6%) | 311 (81.6%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 2 (0.7%) | 2 (0.5%) |
| Ethnicity | |||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 9 (11.0%) | 18 (6.0%) | 27 (7.1%) |
| 0 | 2 (2.4%) | 3 (1.0%) | 5 (1.3%) |
| Non-Spanish; Non-Hispanic | 69 (84.1%) | 257 (86.0%) | 326 (85.6%) |
| Unknown whether Spanish or not | 2 (2.4%) | 18 (6.0%) | 20 (5.2%) |
| Dominican Republic | 0 (0%) | 1 (0.3%) | 1 (0.3%) |
| Puerto Rican | 0 (0%) | 2 (0.7%) | 2 (0.5%) |
| Tumor Purity (%) | |||
| Mean (SD) | 39.6 (15.8) | 39.1 (16.2) | 39.2 (16.1) |
| Median [Min, Max] | 40.0 [5.00, 80.0] | 40.0 [10.0, 90.0] | 40.0 [5.00, 90.0] |
| Missing | 2 (2.4%) | 1 (0.3%) | 3 (0.8%) |
| Cancer Type | |||
| Colon | 23 (28.0%) | 138 (46.2%) | 161 (42.3%) |
| Biliary | 0 (0%) | 6 (2.0%) | 6 (1.6%) |
| Bladder | 7 (8.5%) | 2 (0.7%) | 9 (2.4%) |
| Colorectal | 8 (9.8%) | 15 (5.0%) | 23 (6.0%) |
| CUP | 0 (0%) | 6 (2.0%) | 6 (1.6%) |
| Endometrial | 15 (18.3%) | 68 (22.7%) | 83 (21.8%) |
| Esophagogastric | 4 (4.9%) | 38 (12.7%) | 42 (11.0%) |
| Other | 5 (6.1%) | 2 (0.7%) | 7 (1.8%) |
| Ovarian | 2 (2.4%) | 2 (0.7%) | 4 (1.0%) |
| Pancreas | 3 (3.7%) | 1 (0.3%) | 4 (1.0%) |
| Prostate | 3 (3.7%) | 1 (0.3%) | 4 (1.0%) |
| Rectal | 10 (12.2%) | 10 (3.3%) | 20 (5.2%) |
| Small Bowel | 2 (2.4%) | 10 (3.3%) | 12 (3.1%) |
| Sample Type | |||
| Metastasis | 8 (9.8%) | 37 (12.4%) | 45 (11.8%) |
| Mixed | 7 (8.5%) | 21 (7.0%) | 28 (7.3%) |
| Primary | 67 (81.7%) | 241 (80.6%) | 308 (80.8%) |
With MMRd types collapsed by PMS2 or not| PMS2 (N=264) |
Not_PMS2 (N=117) |
Total (N=381) |
|
|---|---|---|---|
| Age (years) | |||
| Mean (SD) | 67.2 (13.7) | 59.3 (14.6) | 64.8 (14.4) |
| Median [Min, Max] | 70.0 [25.0, 90.0] | 59.0 [26.0, 90.0] | 67.0 [25.0, 90.0] |
| Race | |||
| ASIAN-FAR EAST/INDIAN SUBCONT | 14 (5.3%) | 8 (6.8%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 16 (6.1%) | 6 (5.1%) | 22 (5.8%) |
| NATIVE AMERICAN-AM IND/ALASKA | 2 (0.8%) | 0 (0%) | 2 (0.5%) |
| OTHER | 9 (3.4%) | 6 (5.1%) | 15 (3.9%) |
| PT REFUSED TO ANSWER | 6 (2.3%) | 3 (2.6%) | 9 (2.4%) |
| WHITE | 217 (82.2%) | 94 (80.3%) | 311 (81.6%) |
| Ethnicity | |||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 15 (5.7%) | 12 (10.3%) | 27 (7.1%) |
| 0 | 3 (1.1%) | 2 (1.7%) | 5 (1.3%) |
| Non-Spanish; Non-Hispanic | 226 (85.6%) | 100 (85.5%) | 326 (85.6%) |
| Puerto Rican | 2 (0.8%) | 0 (0%) | 2 (0.5%) |
| Unknown whether Spanish or not | 18 (6.8%) | 2 (1.7%) | 20 (5.2%) |
| Dominican Republic | 0 (0%) | 1 (0.9%) | 1 (0.3%) |
| Tumor Purity (%) | |||
| Mean (SD) | 38.3 (16.1) | 41.1 (16.0) | 39.2 (16.1) |
| Median [Min, Max] | 40.0 [10.0, 90.0] | 40.0 [5.00, 80.0] | 40.0 [5.00, 90.0] |
| Missing | 1 (0.4%) | 2 (1.7%) | 3 (0.8%) |
| Cancer Type | |||
| Colon | 122 (46.2%) | 39 (33.3%) | 161 (42.3%) |
| Biliary | 6 (2.3%) | 0 (0%) | 6 (1.6%) |
| Bladder | 1 (0.4%) | 8 (6.8%) | 9 (2.4%) |
| Colorectal | 11 (4.2%) | 12 (10.3%) | 23 (6.0%) |
| CUP | 5 (1.9%) | 1 (0.9%) | 6 (1.6%) |
| Endometrial | 62 (23.5%) | 21 (17.9%) | 83 (21.8%) |
| Esophagogastric | 33 (12.5%) | 9 (7.7%) | 42 (11.0%) |
| Other | 2 (0.8%) | 5 (4.3%) | 7 (1.8%) |
| Ovarian | 2 (0.8%) | 2 (1.7%) | 4 (1.0%) |
| Pancreas | 1 (0.4%) | 3 (2.6%) | 4 (1.0%) |
| Prostate | 1 (0.4%) | 3 (2.6%) | 4 (1.0%) |
| Rectal | 10 (3.8%) | 10 (8.5%) | 20 (5.2%) |
| Small Bowel | 8 (3.0%) | 4 (3.4%) | 12 (3.1%) |
| Sample Type | |||
| Metastasis | 31 (11.7%) | 14 (12.0%) | 45 (11.8%) |
| Mixed | 18 (6.8%) | 10 (8.5%) | 28 (7.3%) |
| Primary | 215 (81.4%) | 93 (79.5%) | 308 (80.8%) |
#####Groups: Complex, MSH2_MSH6, MLH1_PMS2, MSH6, PMS2, Normal
#####Formula: Feautre ~ MMRd.Type +/* Cancer.Type + Age + Tumor.purity + Race + (1 + MMRd.Type | Metastatic.status)
#####Groups: 1) Singleton: MSH6, PMS2; 2) Multiplex: MSH2_MSH6, MLH1_PMS2, Complex; 3) Normal;
#####Formula: Feautre ~ Multiplex_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + Multiplex_or_not | Metastatic.status)
#####Groups: 1) MSH6: MSH2_MSH6, MSH6; 2) Not_MSH6: MLH1_PMS2, PMS2, Normal
#####Formula: Feautre ~ MSH6_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + MSH6_or_not | Metastatic.status)
#####Groups: 1) PMS2: MLH1_PMS2, PMS2; 2) Not_PMS2: MSH2_MSH6, MSH6, Normal
Feautre ~ PMS2_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + PMS2_or_not | Metastatic.status)
| MSH2_MSH6 (N=9) |
MLH1_PMS2 (N=9) |
PMS2 (N=1) |
MSH6 (N=2) |
? (N=7) |
Total (N=28) |
|
|---|---|---|---|---|---|---|
| Age | ||||||
| Mean (SD) | 50.6 (16.1) | 50.4 (11.9) | 50.0 (NA) | 53.5 (2.12) | 53.4 (9.80) | 51.4 (11.9) |
| Median [Min, Max] | 57.0 [29.0, 71.0] | 52.0 [24.0, 64.0] | 50.0 [50.0, 50.0] | 53.5 [52.0, 55.0] | 52.0 [39.0, 67.0] | 52.0 [24.0, 71.0] |
| Gender | ||||||
| Female | 2 (22.2%) | 4 (44.4%) | 0 (0%) | 0 (0%) | 5 (71.4%) | 11 (39.3%) |
| Male | 7 (77.8%) | 5 (55.6%) | 1 (100%) | 2 (100%) | 2 (28.6%) | 17 (60.7%) |
| Race | ||||||
| Asian | 1 (11.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (3.6%) |
| White | 8 (88.9%) | 8 (88.9%) | 1 (100%) | 2 (100%) | 5 (71.4%) | 24 (85.7%) |
| Unknown | 0 (0%) | 1 (11.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (3.6%) |
| Black or African American | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (28.6%) | 2 (7.1%) |
| Ethnicity | ||||||
| non-Hispanic | 9 (100%) | 7 (77.8%) | 1 (100%) | 2 (100%) | 7 (100%) | 26 (92.9%) |
| Hispanic | 0 (0%) | 2 (22.2%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (7.1%) |
| Lynch.Clinical | ||||||
| No | 1 (11.1%) | 4 (44.4%) | 0 (0%) | 0 (0%) | 2 (28.6%) | 7 (25.0%) |
| UNK | 0 (0%) | 1 (11.1%) | 0 (0%) | 0 (0%) | 1 (14.3%) | 2 (7.1%) |
| Yes | 8 (88.9%) | 4 (44.4%) | 1 (100%) | 2 (100%) | 4 (57.1%) | 19 (67.9%) |
| TumorType | ||||||
| Ampulla of Vater | 2 (22.2%) | 0 (0%) | 0 (0%) | 1 (50.0%) | 0 (0%) | 3 (10.7%) |
| Cholangiocarcinoma | 1 (11.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (3.6%) |
| Colorectal | 3 (33.3%) | 7 (77.8%) | 0 (0%) | 0 (0%) | 5 (71.4%) | 15 (53.6%) |
| Endometrial cancer | 1 (11.1%) | 1 (11.1%) | 0 (0%) | 0 (0%) | 2 (28.6%) | 4 (14.3%) |
| Gastroesophageal cancer | 1 (11.1%) | 0 (0%) | 1 (100%) | 0 (0%) | 0 (0%) | 2 (7.1%) |
| Small Intestine | 1 (11.1%) | 1 (11.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (7.1%) |
| Thyroid | 0 (0%) | 0 (0%) | 0 (0%) | 1 (50.0%) | 0 (0%) | 1 (3.6%) |
| Assembly | ||||||
| hg18 | 7 (77.8%) | 5 (55.6%) | 0 (0%) | 1 (50.0%) | 5 (71.4%) | 18 (64.3%) |
| hg19 | 2 (22.2%) | 4 (44.4%) | 1 (100%) | 1 (50.0%) | 2 (28.6%) | 10 (35.7%) |
MSH2_MSH6 |
MLH1_PMS2 |
PMS2 |
MSH6 |
Overall |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD (N=4) |
SD (N=1) |
PR (N=1) |
CR (N=3) |
PD (N=1) |
SD (N=2) |
PR (N=4) |
CR (N=2) |
PD (N=1) |
NE (N=2) |
NE (N=2) |
PD (N=6) |
SD (N=3) |
PR (N=5) |
CR (N=5) |
|
| Stop_variant | |||||||||||||||
| Mean (SD) | 0 (0) | 0 (NA) | 0 (NA) | 0 (0) | 0 (NA) | 0 (0) | 0 (0) | 0 (0) | 1.00 (NA) | 0 (0) | 0 (0) | 0.167 (0.408) | 0 (0) | 0 (0) | 0 (0) |
| Median [Min, Max] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 1.00 [1.00, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] |
| Start_variant | |||||||||||||||
| Mean (SD) | 0 (0) | 1.00 (NA) | 0 (NA) | 0 (0) | 0 (NA) | 0.500 (0.707) | 0 (0) | 0 (0) | 0 (NA) | 0 (0) | 0 (0) | 0 (0) | 0.667 (0.577) | 0 (0) | 0 (0) |
| Median [Min, Max] | 0 [0, 0] | 1.00 [1.00, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0.500 [0, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 1.00 [0, 1.00] | 0 [0, 0] | 0 [0, 0] |
| Splice_site_donor | |||||||||||||||
| Mean (SD) | 22.5 (11.8) | 88.0 (NA) | 11.0 (NA) | 89.3 (72.5) | 6.00 (NA) | 23.5 (21.9) | 36.0 (7.87) | 25.0 (5.66) | 22.0 (NA) | 24.5 (0.707) | 24.5 (0.707) | 19.7 (11.3) | 45.0 (40.3) | 31.0 (13.1) | 63.6 (62.3) |
| Median [Min, Max] | 27.5 [5.00, 30.0] | 88.0 [88.0, 88.0] | 11.0 [11.0, 11.0] | 49.0 [46.0, 173] | 6.00 [6.00, 6.00] | 23.5 [8.00, 39.0] | 36.5 [26.0, 45.0] | 25.0 [21.0, 29.0] | 22.0 [22.0, 22.0] | 24.5 [24.0, 25.0] | 24.5 [24.0, 25.0] | 24.0 [5.00, 30.0] | 39.0 [8.00, 88.0] | 35.0 [11.0, 45.0] | 46.0 [21.0, 173] |
| Splice_site_acceptor | |||||||||||||||
| Mean (SD) | 103 (68.1) | 22.0 (NA) | 33.0 (NA) | 202 (5.86) | 11.0 (NA) | 80.0 (103) | 152 (34.2) | 119 (4.95) | 24.0 (NA) | 68.5 (50.2) | 68.5 (50.2) | 74.7 (69.0) | 60.7 (80.3) | 128 (60.7) | 169 (46.2) |
| Median [Min, Max] | 129 [5.00, 151] | 22.0 [22.0, 22.0] | 33.0 [33.0, 33.0] | 200 [198, 209] | 11.0 [11.0, 11.0] | 80.0 [7.00, 153] | 155 [110, 186] | 119 [115, 122] | 24.0 [24.0, 24.0] | 68.5 [33.0, 104] | 68.5 [33.0, 104] | 67.0 [5.00, 151] | 22.0 [7.00, 153] | 138 [33.0, 186] | 198 [115, 209] |
| Nonsynonymous_coding | |||||||||||||||
| Mean (SD) | 845 (423) | 3240 (NA) | 203 (NA) | 2100 (1230) | 374 (NA) | 1950 (1300) | 720 (199) | 574 (120) | 1260 (NA) | 1360 (757) | 1360 (757) | 835 (431) | 2380 (1180) | 616 (288) | 1490 (1210) |
| Median [Min, Max] | 728 [472, 1450] | 3240 [3240, 3240] | 203 [203, 203] | 1410 [1360, 3520] | 374 [374, 374] | 1950 [1030, 2870] | 746 [455, 932] | 574 [489, 658] | 1260 [1260, 1260] | 1360 [820, 1890] | 1360 [820, 1890] | 728 [374, 1450] | 2870 [1030, 3240] | 710 [203, 932] | 1360 [489, 3520] |
| Nonsense | |||||||||||||||
| Mean (SD) | 45.8 (31.1) | 65.0 (NA) | 10.0 (NA) | 88.7 (15.8) | 20.0 (NA) | 47.0 (32.5) | 35.5 (14.2) | 36.0 (18.4) | 53.0 (NA) | 67.0 (49.5) | 67.0 (49.5) | 42.7 (26.7) | 53.0 (25.2) | 30.4 (16.8) | 67.6 (32.3) |
| Median [Min, Max] | 37.0 [19.0, 90.0] | 65.0 [65.0, 65.0] | 10.0 [10.0, 10.0] | 85.0 [75.0, 106] | 20.0 [20.0, 20.0] | 47.0 [24.0, 70.0] | 34.0 [20.0, 54.0] | 36.0 [23.0, 49.0] | 53.0 [53.0, 53.0] | 67.0 [32.0, 102] | 67.0 [32.0, 102] | 37.0 [19.0, 90.0] | 65.0 [24.0, 70.0] | 31.0 [10.0, 54.0] | 75.0 [23.0, 106] |
| Inframe_Ins | |||||||||||||||
| Mean (SD) | 2.00 (2.71) | 1.00 (NA) | 0 (NA) | 7.33 (2.52) | 1.00 (NA) | 7.50 (2.12) | 3.50 (0.577) | 4.00 (0) | 1.00 (NA) | 1.00 (1.41) | 1.00 (1.41) | 1.67 (2.16) | 5.33 (4.04) | 2.80 (1.64) | 6.00 (2.55) |
| Median [Min, Max] | 1.00 [0, 6.00] | 1.00 [1.00, 1.00] | 0 [0, 0] | 7.00 [5.00, 10.0] | 1.00 [1.00, 1.00] | 7.50 [6.00, 9.00] | 3.50 [3.00, 4.00] | 4.00 [4.00, 4.00] | 1.00 [1.00, 1.00] | 1.00 [0, 2.00] | 1.00 [0, 2.00] | 1.00 [0, 6.00] | 6.00 [1.00, 9.00] | 3.00 [0, 4.00] | 5.00 [4.00, 10.0] |
| Inframe_Del | |||||||||||||||
| Mean (SD) | 14.0 (11.3) | 5.00 (NA) | 5.00 (NA) | 30.3 (2.52) | 9.00 (NA) | 23.0 (15.6) | 20.8 (6.24) | 20.5 (0.707) | 17.0 (NA) | 4.00 (1.41) | 4.00 (1.41) | 13.7 (9.16) | 17.0 (15.1) | 17.6 (8.88) | 26.4 (5.68) |
| Median [Min, Max] | 10.5 [5.00, 30.0] | 5.00 [5.00, 5.00] | 5.00 [5.00, 5.00] | 30.0 [28.0, 33.0] | 9.00 [9.00, 9.00] | 23.0 [12.0, 34.0] | 21.0 [14.0, 27.0] | 20.5 [20.0, 21.0] | 17.0 [17.0, 17.0] | 4.00 [3.00, 5.00] | 4.00 [3.00, 5.00] | 11.5 [5.00, 30.0] | 12.0 [5.00, 34.0] | 17.0 [5.00, 27.0] | 28.0 [20.0, 33.0] |
| Frameshift | |||||||||||||||
| Mean (SD) | 267 (131) | 537 (NA) | 105 (NA) | 578 (75.6) | 179 (NA) | 273 (326) | 388 (96.1) | 293 (45.3) | 536 (NA) | 102 (91.2) | 102 (91.2) | 297 (159) | 361 (276) | 331 (151) | 464 (167) |
| Median [Min, Max] | 278 [125, 386] | 537 [537, 537] | 105 [105, 105] | 621 [491, 623] | 179 [179, 179] | 273 [42.0, 503] | 394 [273, 489] | 293 [261, 325] | 536 [536, 536] | 102 [37.0, 166] | 102 [37.0, 166] | 278 [125, 536] | 503 [42.0, 537] | 348 [105, 489] | 491 [261, 623] |
NE |
PD |
SD |
PR |
CR |
Overall |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MSH6 (N=2) |
MSH2_MSH6 (N=4) |
MLH1_PMS2 (N=1) |
PMS2 (N=1) |
MSH2_MSH6 (N=1) |
MLH1_PMS2 (N=2) |
MSH2_MSH6 (N=1) |
MLH1_PMS2 (N=4) |
MSH2_MSH6 (N=3) |
MLH1_PMS2 (N=2) |
MSH2_MSH6 (N=9) |
MLH1_PMS2 (N=9) |
PMS2 (N=1) |
MSH6 (N=2) |
|
| Stop_variant | ||||||||||||||
| Mean (SD) | 0 (0) | 0 (0) | 0 (NA) | 1.00 (NA) | 0 (NA) | 0 (0) | 0 (NA) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 1.00 (NA) | 0 (0) |
| Median [Min, Max] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 1.00 [1.00, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 1.00 [1.00, 1.00] | 0 [0, 0] |
| Start_variant | ||||||||||||||
| Mean (SD) | 0 (0) | 0 (0) | 0 (NA) | 0 (NA) | 1.00 (NA) | 0.500 (0.707) | 0 (NA) | 0 (0) | 0 (0) | 0 (0) | 0.111 (0.333) | 0.111 (0.333) | 0 (NA) | 0 (0) |
| Median [Min, Max] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 1.00 [1.00, 1.00] | 0.500 [0, 1.00] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 1.00] | 0 [0, 1.00] | 0 [0, 0] | 0 [0, 0] |
| Splice_site_donor | ||||||||||||||
| Mean (SD) | 24.5 (0.707) | 22.5 (11.8) | 6.00 (NA) | 22.0 (NA) | 88.0 (NA) | 23.5 (21.9) | 11.0 (NA) | 36.0 (7.87) | 89.3 (72.5) | 25.0 (5.66) | 50.8 (51.9) | 27.4 (13.7) | 22.0 (NA) | 24.5 (0.707) |
| Median [Min, Max] | 24.5 [24.0, 25.0] | 27.5 [5.00, 30.0] | 6.00 [6.00, 6.00] | 22.0 [22.0, 22.0] | 88.0 [88.0, 88.0] | 23.5 [8.00, 39.0] | 11.0 [11.0, 11.0] | 36.5 [26.0, 45.0] | 49.0 [46.0, 173] | 25.0 [21.0, 29.0] | 30.0 [5.00, 173] | 29.0 [6.00, 45.0] | 22.0 [22.0, 22.0] | 24.5 [24.0, 25.0] |
| Splice_site_acceptor | ||||||||||||||
| Mean (SD) | 68.5 (50.2) | 103 (68.1) | 11.0 (NA) | 24.0 (NA) | 22.0 (NA) | 80.0 (103) | 33.0 (NA) | 152 (34.2) | 202 (5.86) | 119 (4.95) | 119 (81.1) | 113 (64.0) | 24.0 (NA) | 68.5 (50.2) |
| Median [Min, Max] | 68.5 [33.0, 104] | 129 [5.00, 151] | 11.0 [11.0, 11.0] | 24.0 [24.0, 24.0] | 22.0 [22.0, 22.0] | 80.0 [7.00, 153] | 33.0 [33.0, 33.0] | 155 [110, 186] | 200 [198, 209] | 119 [115, 122] | 147 [5.00, 209] | 122 [7.00, 186] | 24.0 [24.0, 24.0] | 68.5 [33.0, 104] |
| Nonsynonymous_coding | ||||||||||||||
| Mean (SD) | 1360 (757) | 845 (423) | 374 (NA) | 1260 (NA) | 3240 (NA) | 1950 (1300) | 203 (NA) | 720 (199) | 2100 (1230) | 574 (120) | 1460 (1170) | 923 (763) | 1260 (NA) | 1360 (757) |
| Median [Min, Max] | 1360 [820, 1890] | 728 [472, 1450] | 374 [374, 374] | 1260 [1260, 1260] | 3240 [3240, 3240] | 1950 [1030, 2870] | 203 [203, 203] | 746 [455, 932] | 1410 [1360, 3520] | 574 [489, 658] | 1360 [203, 3520] | 710 [374, 2870] | 1260 [1260, 1260] | 1360 [820, 1890] |
| Nonsense | ||||||||||||||
| Mean (SD) | 67.0 (49.5) | 45.8 (31.1) | 20.0 (NA) | 53.0 (NA) | 65.0 (NA) | 47.0 (32.5) | 10.0 (NA) | 35.5 (14.2) | 88.7 (15.8) | 36.0 (18.4) | 58.2 (33.9) | 36.4 (17.7) | 53.0 (NA) | 67.0 (49.5) |
| Median [Min, Max] | 67.0 [32.0, 102] | 37.0 [19.0, 90.0] | 20.0 [20.0, 20.0] | 53.0 [53.0, 53.0] | 65.0 [65.0, 65.0] | 47.0 [24.0, 70.0] | 10.0 [10.0, 10.0] | 34.0 [20.0, 54.0] | 85.0 [75.0, 106] | 36.0 [23.0, 49.0] | 65.0 [10.0, 106] | 31.0 [20.0, 70.0] | 53.0 [53.0, 53.0] | 67.0 [32.0, 102] |
| Inframe_Ins | ||||||||||||||
| Mean (SD) | 1.00 (1.41) | 2.00 (2.71) | 1.00 (NA) | 1.00 (NA) | 1.00 (NA) | 7.50 (2.12) | 0 (NA) | 3.50 (0.577) | 7.33 (2.52) | 4.00 (0) | 3.44 (3.64) | 4.22 (2.22) | 1.00 (NA) | 1.00 (1.41) |
| Median [Min, Max] | 1.00 [0, 2.00] | 1.00 [0, 6.00] | 1.00 [1.00, 1.00] | 1.00 [1.00, 1.00] | 1.00 [1.00, 1.00] | 7.50 [6.00, 9.00] | 0 [0, 0] | 3.50 [3.00, 4.00] | 7.00 [5.00, 10.0] | 4.00 [4.00, 4.00] | 1.00 [0, 10.0] | 4.00 [1.00, 9.00] | 1.00 [1.00, 1.00] | 1.00 [0, 2.00] |
| Inframe_Del | ||||||||||||||
| Mean (SD) | 4.00 (1.41) | 14.0 (11.3) | 9.00 (NA) | 17.0 (NA) | 5.00 (NA) | 23.0 (15.6) | 5.00 (NA) | 20.8 (6.24) | 30.3 (2.52) | 20.5 (0.707) | 17.4 (12.5) | 19.9 (7.91) | 17.0 (NA) | 4.00 (1.41) |
| Median [Min, Max] | 4.00 [3.00, 5.00] | 10.5 [5.00, 30.0] | 9.00 [9.00, 9.00] | 17.0 [17.0, 17.0] | 5.00 [5.00, 5.00] | 23.0 [12.0, 34.0] | 5.00 [5.00, 5.00] | 21.0 [14.0, 27.0] | 30.0 [28.0, 33.0] | 20.5 [20.0, 21.0] | 14.0 [5.00, 33.0] | 20.0 [9.00, 34.0] | 17.0 [17.0, 17.0] | 4.00 [3.00, 5.00] |
| Frameshift | ||||||||||||||
| Mean (SD) | 102 (91.2) | 267 (131) | 179 (NA) | 536 (NA) | 537 (NA) | 273 (326) | 105 (NA) | 388 (96.1) | 578 (75.6) | 293 (45.3) | 383 (204) | 318 (150) | 536 (NA) | 102 (91.2) |
| Median [Min, Max] | 102 [37.0, 166] | 278 [125, 386] | 179 [179, 179] | 536 [536, 536] | 537 [537, 537] | 273 [42.0, 503] | 105 [105, 105] | 394 [273, 489] | 621 [491, 623] | 293 [261, 325] | 386 [105, 623] | 325 [42.0, 503] | 536 [536, 536] | 102 [37.0, 166] |
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